Tropical Storm Lupit made a second landfall early Monday after hitting the Kyushu region the previous day, the weather agency said.
The storm made landfall in Kure, Hiroshima Prefecture, shortly past 5 a.m.
While Lupit became an extratropical cyclone later Monday morning, the weather agency warned of downpours and stormy winds across wide areas. The system is expected to move into the Sea of Japan, bringing heavy rain and strong winds to western, eastern and northern Japan areas through Tuesday, the Meteorological Agency said.
The agency on Monday issued its highest-level rain alert for the town of Kitahiroshima, warning of the threat of floods.
A 46-year-old man in Masuda, Shimane Prefecture went missing after he fell into the swollen Takatsu River while trying to bring a capsized boat closer to the bank at around 6:50 a.m. Monday, according to local police.
Some transportation services suspended operations, with the Sanyo Shinkansen line temporarily halted between Shin-Onomichi and Higashihiroshima stations, according to West Japan Railway Co.
A bridge leading to Kansai Airport in Osaka Prefecture was closed to traffic at around 7:40 a.m. due to projected strong winds.
Rainfall of up to 300 millimeters is projected for the Tokai region, and between 100 mm and 180 mm for wide areas of the country including the Kanto and Kinki regions, in the 24 hours through Tuesday morning.
As of 9 a.m., the system was moving north-northeast over Okayama Prefecture with an atmospheric pressure of 982 hectopascals at its center.